biotite 0.39.0__cp312-cp312-win_amd64.whl → 0.41.0__cp312-cp312-win_amd64.whl

biotite/structure/io/npz/__init__.py

@@ -9,6 +9,9 @@ format is used to store `NumPy` arrays. Since atom arrays and stacks are
 completely built on `NumPy` arrays, this format is preferable for
 Biotite internal usage due to fast I/O operations and preservation
 of all atom annotation arrays.
+
+DEPRECATED: Pickle data directly or use
+:class:`biotite.structure.io.pdbx.BinaryCIFFile` instead.
 """
 
 __name__ = "biotite.structure.io.npz"

biotite/structure/io/npz/file.py

@@ -15,19 +15,22 @@ from ....file import File, is_binary
 class NpzFile(File):
     r"""
     This class represents a NPZ file, the preferable format for
-    Biotite internal structure storage. 
-    
+    Biotite internal structure storage.
+
     Internally the this class writes/reads all attribute arrays of an
     :class:`AtomArray` or :class:`AtomArrayStack` using the *NumPy*
     :func:`save()`/:func:`load()`
     method. This format offers the fastest I/O operations and completely
     preserves the content all atom annotation arrays.
-    
+
+    DEPRECATED: Pickle data directly or use
+    :class:`biotite.structure.io.pdbx.BinaryCIFFile` instead.
+
     Examples
     --------
     Load a \\*.npz file, modify the structure and save the new
     structure into a new file:
-    
+
     >>> import os.path
     >>> file = NpzFile.read(os.path.join(path_to_structures, "1l2y.npz"))
     >>> array_stack = file.get_structure()
@@ -35,30 +38,30 @@ class NpzFile(File):
     >>> file = NpzFile()
     >>> file.set_structure(array_stack_mod)
     >>> file.write(os.path.join(path_to_directory, "1l2y_mod.npz"))
-    
+
     """
-    
+
     def __init__(self):
         super().__init__()
         self._data_dict = None
-    
+
     def __copy_fill__(self, clone):
         super().__copy_fill__(clone)
         if self._data_dict is not None:
             for key, value in self._data_dict.items():
                 clone._data_dict[key] = np.copy(value)
-    
+
     @classmethod
     def read(cls, file):
         """
         Read a NPZ file.
-        
+
         Parameters
         ----------
         file : file-like object or str
             The file to be read.
             Alternatively a file path can be supplied.
-        
+
         Returns
         -------
         file_object : NPZFile
@@ -75,11 +78,11 @@ class NpzFile(File):
                 raise TypeError("A file opened in 'binary' mode is required")
             npz_file._data_dict = dict(np.load(file, allow_pickle=False))
         return npz_file
-                
+
     def write(self, file):
         """
         Write a NPZ file.
-        
+
         Parameters
         ----------
         file : file-like object or str
@@ -93,15 +96,15 @@ class NpzFile(File):
             if not is_binary(file):
                 raise TypeError("A file opened in 'binary' mode is required")
             np.savez(file, **self._data_dict)
-    
+
     def get_structure(self):
         """
         Get an :class:`AtomArray` or :class:`AtomArrayStack` from the
         file.
-        
+
         If this method returns an array or stack depends on which type
         of object was used when the file was written.
-        
+
         Returns
         -------
         array : AtomArray or AtomArrayStack
@@ -117,7 +120,7 @@ class NpzFile(File):
             array = AtomArrayStack(coord.shape[0], coord.shape[1])
         else:
             array = AtomArray(coord.shape[0])
-        
+
         for key, value in self._data_dict.items():
             if key == "coord":
                 array.coord = value
@@ -128,12 +131,12 @@ class NpzFile(File):
             else:
                 array.set_annotation(key, value)
         return array
-        
+
     def set_structure(self, array):
         """
         Set the :class:`AtomArray` or :class:`AtomArrayStack` for the
         file.
-        
+
         Parameters
         ----------
         array : AtomArray or AtomArrayStack

biotite/structure/io/pdb/__init__.py

@@ -6,11 +6,11 @@
 This subpackage is used for reading and writing an :class:`AtomArray` or
 :class:`AtomArrayStack` using the popular PDB format.
 Since this format has some limitations, it will be completely replaced
-someday by the modern PDBx/mmCIF format.
+someday by the modern PDBx format.
 Therefore this subpackage should only be used, if usage of the
-PDBx/mmCIF format is not suitable (e.g. when interfacing
+PDBx (CIF or BinaryCIF) format is not suitable (e.g. when interfacing
 other software).
-In all other cases, usage of the ``pdbx`` subpackage is encouraged.
+In all other cases, usage of the :mod:`pdbx` subpackage is encouraged.
 """
 
 __name__ = "biotite.structure.io.pdb"

biotite/structure/io/pdb/file.py

@@ -12,7 +12,7 @@ from ...atoms import AtomArray, AtomArrayStack, repeat
 from ...bonds import BondList, connect_via_residue_names
 from ...box import vectors_from_unitcell, unitcell_from_vectors
 from ....file import TextFile, InvalidFileError
-from ..general import _guess_element as guess_element
+from ...repair import infer_elements
 from ...error import BadStructureError
 from ...filter import (
     filter_first_altloc,
@@ -23,6 +23,9 @@ from ...util import matrix_rotate
 from .hybrid36 import encode_hybrid36, decode_hybrid36, max_hybrid36_number
 
 
+_PDB_MAX_ATOMS = 99999
+_PDB_MAX_RESIDUES = 9999
+
 # slice objects for readability
 # ATOM/HETATM
 _record = slice(0, 6)
@@ -53,7 +56,8 @@ class PDBFile(TextFile):
     r"""
     This class represents a PDB file.
 
-    The usage of PDBxFile is encouraged in favor of this class.
+    The usage of :mod:`biotite.structure.io.pdbx` is encouraged in favor
+    of this class.
 
     This class only provides support for reading/writing the pure atom
     information (*ATOM*, *HETATM*, *MODEL* and *ENDMDL* records). *TER*
@@ -62,7 +66,8 @@ class PDBFile(TextFile):
 
     See also
     --------
-    PDBxFile
+    CIFFile
+    BinaryCIFFile
 
     Examples
     --------
@@ -458,15 +463,14 @@ class PDBFile(TextFile):
 
         # Replace empty strings for elements with guessed types
         # This is used e.g. for PDB files created by Gromacs
-        if "" in array.element:
-            rep_num = 0
-            for idx in range(len(array.element)):
-                if not array.element[idx]:
-                    atom_name = array.atom_name[idx]
-                    array.element[idx] = guess_element(atom_name)
-                    rep_num += 1
+        empty_element_mask = array.element == ""
+        if empty_element_mask.any():
             warnings.warn(
-                "{} elements were guessed from atom_name.".format(rep_num)
+                f"{np.count_nonzero(empty_element_mask)} elements "
+                "were guessed from atom name"
+            )
+            array.element[empty_element_mask] = infer_elements(
+                array.atom_name[empty_element_mask]
             )
 
         # Fill in coordinates
@@ -510,7 +514,7 @@ class PDBFile(TextFile):
                     warnings.warn(
                         "File contains invalid 'CRYST1' record, box is ignored"
                     )
-                    box = None
+                    break
 
                 if isinstance(array, AtomArray):
                     array.box = box
@@ -572,6 +576,8 @@ class PDBFile(TextFile):
         records are also written for all non-water hetero residues
         and all inter-residue connections.
         """
+        _check_pdb_compatibility(array, hybrid36)
+
         natoms = array.array_length()
         annot_categories = array.get_annotation_categories()
         record = np.char.array(np.where(array.hetero, "HETATM", "ATOM"))
@@ -597,25 +603,6 @@ class PDBFile(TextFile):
         else:
             charge = np.char.array(np.full(natoms, "  ", dtype="U2"))
 
-        # Do checks on atom array (stack)
-        if hybrid36:
-            max_atoms = max_hybrid36_number(5)
-            max_residues = max_hybrid36_number(4)
-        else:
-            max_atoms, max_residues = 99999, 9999
-        if array.array_length() > max_atoms:
-            warnings.warn(f"More then {max_atoms:,} atoms per model")
-        if (array.res_id > max_residues).any():
-            warnings.warn(f"Residue IDs exceed {max_residues:,}")
-        if np.isnan(array.coord).any():
-            raise BadStructureError("Coordinates contain 'NaN' values")
-        if any([len(name) > 1 for name in array.chain_id]):
-            raise BadStructureError("Some chain IDs exceed 1 character")
-        if any([len(name) > 3 for name in array.res_name]):
-            raise BadStructureError("Some residue names exceed 3 characters")
-        if any([len(name) > 4 for name in array.atom_name]):
-            raise BadStructureError("Some atom names exceed 4 characters")
-
         if hybrid36:
             pdb_atom_id = np.char.array(
                 [encode_hybrid36(i, 5) for i in atom_id]
@@ -628,14 +615,14 @@ class PDBFile(TextFile):
             # but negative IDs are also possible
             pdb_atom_id = np.char.array(np.where(
                 atom_id > 0,
-                ((atom_id - 1) % 99999) + 1,
+                ((atom_id - 1) % _PDB_MAX_ATOMS) + 1,
                 atom_id
             ).astype(str))
             # Residue IDs are supported up to 9999,
             # but negative IDs are also possible
             pdb_res_id = np.char.array(np.where(
                 array.res_id > 0,
-                ((array.res_id - 1) % 9999) + 1,
+                ((array.res_id - 1) % _PDB_MAX_RESIDUES) + 1,
                 array.res_id
             ).astype(str))
 
@@ -1182,4 +1169,72 @@ def _apply_transformations(structure, rotations, translations):
         coord += translation
         assembly_coord[i] = coord
 
-    return repeat(structure, assembly_coord)
+    return repeat(structure, assembly_coord)
+
+
+def _check_pdb_compatibility(array, hybrid36):
+    annot_categories = array.get_annotation_categories()
+
+    if hybrid36:
+        max_atoms = max_hybrid36_number(5)
+        max_residues = max_hybrid36_number(4)
+    else:
+        max_atoms, max_residues = _PDB_MAX_ATOMS, _PDB_MAX_RESIDUES
+    if "atom_id" in annot_categories:
+        max_atom_id = np.max(array.atom_id)
+    else:
+        max_atom_id = array.array_length()
+
+    if max_atom_id > max_atoms:
+        warnings.warn(f"Atom IDs exceed {max_atoms:,}, will be wrapped")
+    if (array.res_id > max_residues).any():
+        warnings.warn(f"Residue IDs exceed {max_residues:,}, will be wrapped")
+    if np.isnan(array.coord).any():
+        raise BadStructureError("Coordinates contain 'NaN' values")
+    if any([len(name) > 1 for name in array.chain_id]):
+        raise BadStructureError("Some chain IDs exceed 1 character")
+    if any([len(name) > 3 for name in array.res_name]):
+        raise BadStructureError("Some residue names exceed 3 characters")
+    if any([len(name) > 4 for name in array.atom_name]):
+        raise BadStructureError("Some atom names exceed 4 characters")
+    for i, coord_name in enumerate(["x", "y", "z"]):
+        n_coord_digits = _number_of_integer_digits(array.coord[..., i])
+        if n_coord_digits > 4:
+            raise BadStructureError(
+                f"4 pre-decimal columns for {coord_name}-coordinates are "
+                f"available, but array would require {n_coord_digits}"
+            )
+    if "b_factor" in annot_categories:
+        n_b_factor_digits = _number_of_integer_digits(array.b_factor)
+        if n_b_factor_digits > 3:
+            raise BadStructureError(
+                "3 pre-decimal columns for B-factor are available, "
+                f"but array would require {n_b_factor_digits}"
+            )
+    if "occupancy" in annot_categories:
+        n_occupancy_digits = _number_of_integer_digits(array.occupancy)
+        if n_occupancy_digits > 3:
+            raise BadStructureError(
+                "3 pre-decimal columns for occupancy are available, "
+                f"but array would require {n_occupancy_digits}"
+            )
+    if "charge" in annot_categories:
+        # The sign can be omitted is it is put into the adjacent column
+        n_charge_digits = _number_of_integer_digits(np.abs(array.charge))
+        if n_charge_digits > 1:
+            raise BadStructureError(
+                "1 column for charge is available, "
+                f"but array would require {n_charge_digits}"
+            )
+
+
+def _number_of_integer_digits(values):
+    """
+    Get the maximum number of characters needed to represent the
+    pre-decimal positions of the given numeric values.
+    """
+    values = values.astype(int, copy=False)
+    n_digits = 0
+    n_digits = max(n_digits, len(str(np.min(values))))
+    n_digits = max(n_digits, len(str(np.max(values))))
+    return n_digits

biotite/structure/io/pdb/hybrid36.c

@@ -1,4 +1,4 @@
-/* Generated by Cython 3.0.7 */
+/* Generated by Cython 3.0.10 */
 
 /* BEGIN: Cython Metadata
 {
@@ -36,10 +36,10 @@ END: Cython Metadata */
 #else
 #define __PYX_EXTRA_ABI_MODULE_NAME ""
 #endif
-#define CYTHON_ABI "3_0_7" __PYX_EXTRA_ABI_MODULE_NAME
+#define CYTHON_ABI "3_0_10" __PYX_EXTRA_ABI_MODULE_NAME
 #define __PYX_ABI_MODULE_NAME "_cython_" CYTHON_ABI
 #define __PYX_TYPE_MODULE_PREFIX __PYX_ABI_MODULE_NAME "."
-#define CYTHON_HEX_VERSION 0x030007F0
+#define CYTHON_HEX_VERSION 0x03000AF0
 #define CYTHON_FUTURE_DIVISION 1
 #include <stddef.h>
 #ifndef offsetof
@@ -131,6 +131,8 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
   #endif
+  #undef CYTHON_USE_FREELISTS
+  #define CYTHON_USE_FREELISTS 0
 #elif defined(PYPY_VERSION)
   #define CYTHON_COMPILING_IN_PYPY 1
   #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -192,6 +194,8 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
   #endif
+  #undef CYTHON_USE_FREELISTS
+  #define CYTHON_USE_FREELISTS 0
 #elif defined(CYTHON_LIMITED_API)
   #ifdef Py_LIMITED_API
     #undef __PYX_LIMITED_VERSION_HEX
@@ -253,6 +257,8 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
   #endif
+  #undef CYTHON_USE_FREELISTS
+  #define CYTHON_USE_FREELISTS 0
 #elif defined(Py_GIL_DISABLED) || defined(Py_NOGIL)
   #define CYTHON_COMPILING_IN_PYPY 0
   #define CYTHON_COMPILING_IN_CPYTHON 0
@@ -262,11 +268,17 @@ END: Cython Metadata */
   #ifndef CYTHON_USE_TYPE_SLOTS
     #define CYTHON_USE_TYPE_SLOTS 1
   #endif
+  #ifndef CYTHON_USE_TYPE_SPECS
+    #define CYTHON_USE_TYPE_SPECS 0
+  #endif
   #undef CYTHON_USE_PYTYPE_LOOKUP
   #define CYTHON_USE_PYTYPE_LOOKUP 0
   #ifndef CYTHON_USE_ASYNC_SLOTS
     #define CYTHON_USE_ASYNC_SLOTS 1
   #endif
+  #ifndef CYTHON_USE_PYLONG_INTERNALS
+    #define CYTHON_USE_PYLONG_INTERNALS 0
+  #endif
   #undef CYTHON_USE_PYLIST_INTERNALS
   #define CYTHON_USE_PYLIST_INTERNALS 0
   #ifndef CYTHON_USE_UNICODE_INTERNALS
@@ -274,8 +286,6 @@ END: Cython Metadata */
   #endif
   #undef CYTHON_USE_UNICODE_WRITER
   #define CYTHON_USE_UNICODE_WRITER 0
-  #undef CYTHON_USE_PYLONG_INTERNALS
-  #define CYTHON_USE_PYLONG_INTERNALS 0
   #ifndef CYTHON_AVOID_BORROWED_REFS
     #define CYTHON_AVOID_BORROWED_REFS 0
   #endif
@@ -287,11 +297,22 @@ END: Cython Metadata */
   #endif
   #undef CYTHON_FAST_THREAD_STATE
   #define CYTHON_FAST_THREAD_STATE 0
+  #undef CYTHON_FAST_GIL
+  #define CYTHON_FAST_GIL 0
+  #ifndef CYTHON_METH_FASTCALL
+    #define CYTHON_METH_FASTCALL 1
+  #endif
   #undef CYTHON_FAST_PYCALL
   #define CYTHON_FAST_PYCALL 0
+  #ifndef CYTHON_PEP487_INIT_SUBCLASS
+    #define CYTHON_PEP487_INIT_SUBCLASS 1
+  #endif
   #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
     #define CYTHON_PEP489_MULTI_PHASE_INIT 1
   #endif
+  #ifndef CYTHON_USE_MODULE_STATE
+    #define CYTHON_USE_MODULE_STATE 0
+  #endif
   #ifndef CYTHON_USE_TP_FINALIZE
     #define CYTHON_USE_TP_FINALIZE 1
   #endif
@@ -299,6 +320,12 @@ END: Cython Metadata */
   #define CYTHON_USE_DICT_VERSIONS 0
   #undef CYTHON_USE_EXC_INFO_STACK
   #define CYTHON_USE_EXC_INFO_STACK 0
+  #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+    #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
+  #endif
+  #ifndef CYTHON_USE_FREELISTS
+    #define CYTHON_USE_FREELISTS 0
+  #endif
 #else
   #define CYTHON_COMPILING_IN_PYPY 0
   #define CYTHON_COMPILING_IN_CPYTHON 1
@@ -389,6 +416,9 @@ END: Cython Metadata */
   #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
     #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
   #endif
+  #ifndef CYTHON_USE_FREELISTS
+    #define CYTHON_USE_FREELISTS 1
+  #endif
 #endif
 #if !defined(CYTHON_FAST_PYCCALL)
 #define CYTHON_FAST_PYCCALL  (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
@@ -581,14 +611,14 @@ END: Cython Metadata */
         PyObject *exception_table = NULL;
         PyObject *types_module=NULL, *code_type=NULL, *result=NULL;
         #if __PYX_LIMITED_VERSION_HEX < 0x030B0000
-        PyObject *version_info; // borrowed
+        PyObject *version_info;
         PyObject *py_minor_version = NULL;
         #endif
         long minor_version = 0;
         PyObject *type, *value, *traceback;
         PyErr_Fetch(&type, &value, &traceback);
         #if __PYX_LIMITED_VERSION_HEX >= 0x030B0000
-        minor_version = 11; // we don't yet need to distinguish between versions > 11
+        minor_version = 11;
         #else
         if (!(version_info = PySys_GetObject("version_info"))) goto end;
         if (!(py_minor_version = PySequence_GetItem(version_info, 1))) goto end;
@@ -646,7 +676,7 @@ END: Cython Metadata */
                                                     PyObject *fv, PyObject *cell, PyObject* fn,
                                                     PyObject *name, int fline, PyObject *lnos) {
     PyCodeObject *result;
-    PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);  // we don't have access to __pyx_empty_bytes here
+    PyObject *empty_bytes = PyBytes_FromStringAndSize("", 0);
     if (!empty_bytes) return NULL;
     result =
       #if PY_VERSION_HEX >= 0x030C0000
@@ -732,8 +762,13 @@ END: Cython Metadata */
   typedef PyObject *(*__Pyx_PyCFunctionFastWithKeywords) (PyObject *self, PyObject *const *args,
                                                           Py_ssize_t nargs, PyObject *kwnames);
 #else
-  #define __Pyx_PyCFunctionFast _PyCFunctionFast
-  #define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
+  #if PY_VERSION_HEX >= 0x030d00A4
+  #  define __Pyx_PyCFunctionFast PyCFunctionFast
+  #  define __Pyx_PyCFunctionFastWithKeywords PyCFunctionFastWithKeywords
+  #else
+  #  define __Pyx_PyCFunctionFast _PyCFunctionFast
+  #  define __Pyx_PyCFunctionFastWithKeywords _PyCFunctionFastWithKeywords
+  #endif
 #endif
 #if CYTHON_METH_FASTCALL
   #define __Pyx_METH_FASTCALL METH_FASTCALL
@@ -1085,7 +1120,7 @@ static CYTHON_INLINE PyObject * __Pyx_PyDict_GetItemStrWithError(PyObject *dict,
   #define __Pyx_PyBytes_GET_SIZE(o) PyBytes_Size(o)
   #define __Pyx_PyByteArray_GET_SIZE(o) PyByteArray_Size(o)
 #endif
-#if PY_VERSION_HEX >= 0x030d00A1
+#if __PYX_LIMITED_VERSION_HEX >= 0x030d00A1
   #define __Pyx_PyImport_AddModuleRef(name) PyImport_AddModuleRef(name)
 #else
   static CYTHON_INLINE PyObject *__Pyx_PyImport_AddModuleRef(const char *name) {
@@ -1172,7 +1207,7 @@ static CYTHON_INLINE float __PYX_NAN() {
 #endif
 
 #define __PYX_MARK_ERR_POS(f_index, lineno) \
-    { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__; (void)__pyx_clineno; }
+    { __pyx_filename = __pyx_f[f_index]; (void)__pyx_filename; __pyx_lineno = lineno; (void)__pyx_lineno; __pyx_clineno = __LINE__;  (void)__pyx_clineno; }
 #define __PYX_ERR(f_index, lineno, Ln_error) \
     { __PYX_MARK_ERR_POS(f_index, lineno) goto Ln_error; }
 
@@ -1278,24 +1313,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
 #define __Pyx_PyByteArray_FromCString(s)   __Pyx_PyByteArray_FromString((const char*)s)
 #define __Pyx_PyStr_FromCString(s)     __Pyx_PyStr_FromString((const char*)s)
 #define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
-#if CYTHON_COMPILING_IN_LIMITED_API
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const wchar_t *u)
-{
-    const wchar_t *u_end = u;
-    while (*u_end++) ;
-    return (size_t)(u_end - u - 1);
-}
-#else
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
-    const Py_UNICODE *u_end = u;
-    while (*u_end++) ;
-    return (size_t)(u_end - u - 1);
-}
-#endif
 #define __Pyx_PyUnicode_FromOrdinal(o)       PyUnicode_FromOrdinal((int)o)
-#define __Pyx_PyUnicode_FromUnicode(u)       PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
 #define __Pyx_PyUnicode_AsUnicode            PyUnicode_AsUnicode
 #define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
 #define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
@@ -1345,7 +1363,7 @@ static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
   #endif
   typedef Py_ssize_t  __Pyx_compact_pylong;
   typedef size_t  __Pyx_compact_upylong;
-  #else  // Py < 3.12
+  #else
   #define __Pyx_PyLong_IsNeg(x)  (Py_SIZE(x) < 0)
   #define __Pyx_PyLong_IsNonNeg(x)  (Py_SIZE(x) >= 0)
   #define __Pyx_PyLong_IsZero(x)  (Py_SIZE(x) == 0)
@@ -1916,8 +1934,8 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int
     #define __Pyx_Arg_NewRef_VARARGS(arg) __Pyx_NewRef(arg)
     #define __Pyx_Arg_XDECREF_VARARGS(arg) Py_XDECREF(arg)
 #else
-    #define __Pyx_Arg_NewRef_VARARGS(arg) arg // no-op
-    #define __Pyx_Arg_XDECREF_VARARGS(arg) // no-op - arg is borrowed
+    #define __Pyx_Arg_NewRef_VARARGS(arg) arg
+    #define __Pyx_Arg_XDECREF_VARARGS(arg)
 #endif
 #define __Pyx_NumKwargs_VARARGS(kwds) PyDict_Size(kwds)
 #define __Pyx_KwValues_VARARGS(args, nargs) NULL
@@ -1933,8 +1951,9 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int
   #else
     #define __Pyx_KwargsAsDict_FASTCALL(kw, kwvalues) _PyStack_AsDict(kwvalues, kw)
   #endif
-    #define __Pyx_Arg_NewRef_FASTCALL(arg) arg // no-op, __Pyx_Arg_FASTCALL is direct and this needs
-    #define __Pyx_Arg_XDECREF_FASTCALL(arg)  // no-op - arg was returned from array
+    #define __Pyx_Arg_NewRef_FASTCALL(arg) arg  /* no-op, __Pyx_Arg_FASTCALL is direct and this needs
+                                                   to have the same reference counting */
+    #define __Pyx_Arg_XDECREF_FASTCALL(arg)
 #else
     #define __Pyx_Arg_FASTCALL __Pyx_Arg_VARARGS
     #define __Pyx_NumKwargs_FASTCALL __Pyx_NumKwargs_VARARGS
@@ -2571,7 +2590,7 @@ typedef struct {
 #endif
     void *defaults;
     int defaults_pyobjects;
-    size_t defaults_size;  // used by FusedFunction for copying defaults
+    size_t defaults_size;
     int flags;
     PyObject *defaults_tuple;
     PyObject *defaults_kwdict;
@@ -22004,11 +22023,11 @@ static CYTHON_INLINE PyObject * __Pyx_GetKwValue_FASTCALL(PyObject *kwnames, PyO
     {
         int eq = __Pyx_PyUnicode_Equals(s, PyTuple_GET_ITEM(kwnames, i), Py_EQ);
         if (unlikely(eq != 0)) {
-            if (unlikely(eq < 0)) return NULL;  // error
+            if (unlikely(eq < 0)) return NULL;
             return kwvalues[i];
         }
     }
-    return NULL;  // not found (no exception set)
+    return NULL;
 }
 #if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x030d0000
 CYTHON_UNUSED static PyObject *__Pyx_KwargsAsDict_FASTCALL(PyObject *kwnames, PyObject *const *kwvalues) {
@@ -22121,7 +22140,7 @@ static int __Pyx_ParseOptionalKeywords(
         if (*name) {
             values[name-argnames] = value;
 #if CYTHON_AVOID_BORROWED_REFS
-            Py_INCREF(value); // transfer ownership of value to values
+            Py_INCREF(value);
             Py_DECREF(key);
 #endif
             key = NULL;
@@ -22140,7 +22159,7 @@ static int __Pyx_ParseOptionalKeywords(
                         && _PyString_Eq(**name, key)) {
                     values[name-argnames] = value;
 #if CYTHON_AVOID_BORROWED_REFS
-                    value = NULL;  // ownership transferred to values
+                    value = NULL;
 #endif
                     break;
                 }
@@ -22172,7 +22191,7 @@ static int __Pyx_ParseOptionalKeywords(
                 if (cmp == 0) {
                     values[name-argnames] = value;
 #if CYTHON_AVOID_BORROWED_REFS
-                    value = NULL; // ownership transferred to values
+                    value = NULL;
 #endif
                     break;
                 }
@@ -24164,9 +24183,10 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes(
 
 /* UnpackUnboundCMethod */
 static PyObject *__Pyx_SelflessCall(PyObject *method, PyObject *args, PyObject *kwargs) {
+    PyObject *result;
     PyObject *selfless_args = PyTuple_GetSlice(args, 1, PyTuple_Size(args));
     if (unlikely(!selfless_args)) return NULL;
-    PyObject *result = PyObject_Call(method, selfless_args, kwargs);
+    result = PyObject_Call(method, selfless_args, kwargs);
     Py_DECREF(selfless_args);
     return result;
 }
@@ -26131,7 +26151,7 @@ static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(PyObject *func,
     default:
         return NULL;
     }
-    return ((_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
+    return ((__Pyx_PyCFunctionFastWithKeywords)(void(*)(void))def->ml_meth)(self, args, nargs, kwnames);
 }
 static PyObject * __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS_METHOD(PyObject *func, PyObject *const *args, size_t nargsf, PyObject *kwnames)
 {
@@ -26590,7 +26610,7 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
     #else
     py_code = PyCode_NewEmpty(filename, funcname, py_line);
     #endif
-    Py_XDECREF(py_funcname);  // XDECREF since it's only set on Py3 if cline
+    Py_XDECREF(py_funcname);
     return py_code;
 bad:
     Py_XDECREF(py_funcname);